## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
| patient | ID | age_at_sample_exact | cell_type | phase | BaitLabel | |
|---|---|---|---|---|---|---|
| 2 | PD9478 | PD9478dd | 54.17112 | BM Gran | Recapture | PD9478dd |
| 3 | PD9478 | PD9478de | 54.80630 | PB Gran | Recapture | PD9478de |
| 4 | PD9478 | PD9478df | 55.37851 | PB Gran | Recapture | PD9478df |
| 5 | PD9478 | PD9478dg | 61.71663 | PB Gran | Recapture | PD9478dg |
| 6 | PD9478 | PD9478dh | 63.23066 | PB Gran | Recapture | PD9478dh |
| 7 | PD9478 | PD9478di | 63.99726 | PB Gran | Recapture | PD9478di |
| 8 | PD9478 | PD9478dj | 66.42847 | PB Gran | Recapture | PD9478dj |
| 9 | PD9478 | PD9478dk | 66.96783 | PB Gran | Recapture | PD9478dk |
| 10 | PD9478 | PD9478dl | 67.57016 | PB Gran | Recapture | PD9478dl |
| 11 | PD9478 | PD9478dm | 68.02190 | PB Gran | Recapture | PD9478dm |
| 1 | PD9478 | COLONY68 | 68.02464 | BFU-E-Colony | Colony | NA |
| 12 | PD9478 | PD9478dn | 70.03422 | PB Gran | Recapture | PD9478dn |
| 13 | PD9478 | PD9478do | 70.51335 | PB Gran | Recapture | PD9478do |
| 14 | PD9478 | PD9478dp | 71.04723 | BM Gran | Recapture | PD9478dp |
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)
Note that the different colours on the tree indicate the separately fitted mutation rate clades.
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## 0.0000 -0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 18.4230 0.5524 33.3516 <.0001 17.3403 19.5056 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
| node | driver | status | child_count | type | colony_count | mean_lambda_rescaled | correction | sd_rescaled | lb_rescaled | ub_rescaled | median_rescaled | p_lt_wt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -1 | WT | 1 | -1 | local | 8 | 18.42296 | 1.016185 | 0.3051312 | 17.84271 | 19.04460 | 18.41553 | NA |
| 85 | JAK2 | 1 | 72 | local | 68 | 19.02647 | 1.016185 | 0.4951584 | 18.06907 | 20.01525 | 19.01747 | 0.155525 |
| 67 | 9pUPD:DNMT3A:JAK2 | 0 | 1 | local | 1 | 22.06799 | 1.016185 | 3.3529333 | 15.17648 | 28.91798 | 22.01345 | 0.115275 |
| 24 | 9pUPD:DNMT3A:JAK2 | 0 | 1 | local | 1 | 17.73788 | 1.016185 | 3.3688803 | 10.90467 | 25.01563 | 17.66711 | 0.606175 |
| 72 | 9pUPD:JAK2 | 0 | 1 | local | 1 | 21.40554 | 1.016185 | 2.8711780 | 15.67051 | 27.84762 | 21.12540 | 0.097375 |
| 3 | 9pUPD:DNMT3A:JAK2 | 0 | 1 | local | 1 | 21.71461 | 1.016185 | 3.3140179 | 14.88753 | 28.45361 | 21.66772 | 0.133775 |
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
| patient | node | driver | child_count | lower_median | upper_median | lower_lb95 | lower_ub95 | upper_lb95 | upper_ub95 | N | group | age_at_diagnosis_pcy | max_age_at_sample | min_age_at_sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD9478 | 85 | JAK2 | 72 | 0.0222469 | 10.05039 | 0.0149079 | 0.0438736 | 8.618587 | 11.62251 | 14 | JAK2 | 53.76865 | 71.7755 | 54.89938 |
| PD9478 | 86 | DNMT3A | 71 | 10.0503937 | 45.65464 | 8.6185874 | 11.6225101 | 44.425247 | 46.83687 | 14 | DNMT3A | 53.76865 | 71.7755 | 54.89938 |
## Timings using the Clade Specific Rates
| label | node | het.sensitivity | chr | start | end | nhet | nhom | mean_loh_event | lower_loh_event | upper_loh_event | t_before_end | t_before_end_lower | t_before_end_upper | kb | count_in_bin | count_se | pmut | pmut_se | xmean | xse_mean | xsd | x2.5. | x50. | x97.5. | xn_eff | xRhat | lmean | lse_mean | patient | driver3 | child_count |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9pUPD_A | 67 | 0.7262 | 9 | 10469 | 34110846 | 2 | 0 | NA | NA | NA | NA | NA | NA | 34100000 | 6765 | 82.25 | 0.01477 | 0.0001796 | 0.2903 | 0.0012951 | 0.2097 | 0.011412 | 0.2503 | 0.7573 | 26205 | 1 | 4.297 | 0.0003602 | NA | NA | NA |
| 9pUPD_B | 24 | 0.8921 | 9 | 10469 | 35005250 | 1 | 0 | NA | NA | NA | NA | NA | NA | 35000000 | 6891 | 83.01 | 0.01505 | 0.0001813 | 0.4367 | 0.0016423 | 0.2533 | 0.022671 | 0.4274 | 0.9014 | 23787 | 1 | 4.357 | 0.0003602 | NA | NA | NA |
| 9pUPD_C | 72 | 0.8973 | 9 | 10469 | 34098110 | 12 | 8 | NA | NA | NA | NA | NA | NA | 34000000 | 6753 | 82.18 | 0.01475 | 0.0001795 | 0.4779 | 0.0006041 | 0.1041 | 0.273510 | 0.4782 | 0.6782 | 29708 | 1 | 16.086 | 0.0011325 | NA | NA | NA |
| 9pUPD_D | 3 | 0.6717 | 9 | 10469 | 34107232 | 5 | 0 | NA | NA | NA | NA | NA | NA | 34100000 | 6765 | 82.25 | 0.01477 | 0.0001796 | 0.1605 | 0.0008847 | 0.1339 | 0.004867 | 0.1262 | 0.4950 | 22912 | 1 | 6.137 | 0.0005490 | NA | NA | NA |
Here we exclude all local CNAs and depict as color VAF plots